When the load is finished, pressing "Genome View" will launch the genome viewer (JBrowse).

Note: The length of time it takes to load annotations depends on the load on the database and the number of annotations being loaded. For this example (and no load on the server), it should take ~ 3-5 minutes.

When the load is finished, pressing "Genome View" will launch the genome viewer (JBrowse).

Note: The length of time it takes to load annotations depends on the load on the database and the number of annotations being loaded. For this example (and no load on the server), it should take ~ 10-20 minutes.

CoGe should automatically detect the type of file, but you can always set it. The supported file types are available here

Press Next

The options presented depend on the detected file type. For these dataset, you can skip this step.

Press Next

Review the data and associated information.

Press "Start Loading" to start the loading the data.

When finished, there is a link to the experiment you loaded. From there, you can get detailed information on the experiment (and modify what you've entered) in ExperimentView

From ExperimentView, you can launch the genome browser by pressing "View"

Visualizing data you just loaded

From your profile page, double click on the genome (or experiment) you loaded

Press "Browse". This will launch CoGe's implementation of JBrowse: GenomeView

You can select tracks to visualize in the menu on the right

RNASeq Processing

EPIC-CoGe has a variety of pipelines for processing FastQ data. Its Expression Analysis Pipeline will clean your reads, map them, quantify their abundance to position in the genome, and quantify their abundance per transcript as FPKM values.

Note: You can add private experimental data to public genomes (Mix and match public and private data)